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• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB27_M

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB27_M

  Dataset EGAD00001001720

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB27_F

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB27_F

  Dataset EGAD00001001719

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB27_C

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB27_C

  Dataset EGAD00001001718

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB25_M

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB25_M

  Dataset EGAD00001001717

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB25_F

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB25_F

  Dataset EGAD00001001716

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB25_C

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB25_C

  Dataset EGAD00001001715

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB24_M

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB24_M

  Dataset EGAD00001001714

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB24_C

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB24_C

  Dataset EGAD00001001712

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB23_M

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB23_M

  Dataset EGAD00001001711

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB10_C

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB10_C

  Dataset EGAD00001001694

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB10_F

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB10_F

  Dataset EGAD00001001695

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB10_M

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB10_M

  Dataset EGAD00001001696

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB15_C

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB15_C

  Dataset EGAD00001001697

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB15_F

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB15_F

  Dataset EGAD00001001698

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB15_M

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB15_M

  Dataset EGAD00001001699

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB1_C

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB1_C

  Dataset EGAD00001001700

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB1_F

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB1_F

  Dataset EGAD00001001701

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB1_M

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB1_M

  Dataset EGAD00001001702

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB21_C

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB21_C

  Dataset EGAD00001001703

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB21_F

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB21_F

  Dataset EGAD00001001704

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB21_M

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB21_M

  Dataset EGAD00001001705

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB22_F

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB22_F

  Dataset EGAD00001001707

• Whole exome sequencing for HELIC

  The HELIC study has been whole genome sequencing individuals from 2 Greek isolatedpopulations at 1x depth. The genotype calling process crucially involves a VQSR stepfollowed by imputation-based refinement. We have been investigating optimal ways toincrease calling accuracy. To aid us in setting appropriate parameters for VQSR and otherQC steps, we have carried out whole exome sequencing of a small number ofHELIC samples.

  Dataset EGAD00001001638

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB22_C

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB22_C

  Dataset EGAD00001001706

• Transcriptome and Exome from longitudinal samples of human glioblastoma (newly added after 2015)

  We expanded our previous collection of longitudinal GBM patients (EGAS00001001041) by recruiting 21 additional patients. Tumor specimens were subjected to whole-exome sequencing (16 of 21 cases, with the matched normal/blood) and transcriptome sequencing (16 of 21 cases).

  Dataset EGAD00001002143

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB51_M

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB51_M

  Dataset EGAD00001001762

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB52_F

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB52_F

  Dataset EGAD00001001764

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB55_C

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB55_C

  Dataset EGAD00001001766

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB55_M

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB55_M

  Dataset EGAD00001001768

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB58_F

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB58_F

  Dataset EGAD00001001773

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB58_M

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB58_M

  Dataset EGAD00001001774

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB8_C

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB8_C

  Dataset EGAD00001001781

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: BvB8_M

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: BvB8_M

  Dataset EGAD00001001783

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW14_F

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW14_F

  Dataset EGAD00001001788

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW20_C

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW20_C

  Dataset EGAD00001001796

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW22_C

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW22_C

  Dataset EGAD00001001799

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW2_M

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW2_M

  Dataset EGAD00001001813

• WGS of 50 Intellectual Disability (ID) trios with Complete Genomics Sequencing. Dataset of sample: MW32_C

  50 trios were whole genome sequenced with Complete Genomics to a depth of 80x. For each trio the child was affected with severe ID, and the parents were unaffected. All trios were negative for array, targeted gene and whole exome screening. Dataset consists of sample: MW32_C

  Dataset EGAD00001001814

• Congenital anosmia 2

  Congenital anosmias can be complete (the lack of a sense of smell) or specific (the inability to detect specific smells). Here we obtained genomic DNA from families with multiple individuals with anosmia, suggesting they are congenital. These include those inherited in a manner consistent with dominant and recessive alleles. We have sequenced the exomes of both affected and unaffected family members on the Illumina platform.

  Dataset EGAD00001002228

• ETMR ATACSeq

  ATACSeq library amplification was performed on 5 ETMR tumour samples using the NEBnext High Fidelity 2xPCR Master Mix (New England Biolabs, Cat#M0541S) according to the manufacturer’s protocol. ATAC-seq libraries were sequenced using single-end 50 bp reads on the Illumina HiSeq 2000 platform. ATAC-seq peaks analysed was conducted as published previously(Torchia et al. 2016).

  Dataset EGAD00001004805

• Mutant clone mapping in normal oesophagus (2019-04-03)

  We will use targeted exome sequencing to examine normal appearing epithelium and whole exome and whole genome sequencing of microdissected clones identified by immunostaining Some of the samples will be of low DNA concentration and therefore may require extra rounds of amplification during library prep. . This dataset contains all the data available for this study on 2019-04-03.

  Dataset EGAD00001004888

• Single-cell TCR sequencing of DQ2.2-glut-L1-specific T cells

  In order to characterize the T cell receptor (TCR) repertoire of DQ2.2-glut-L1-specific T cells, we performed high-throughput DNA sequencing of rearranged TCR-α and TCR-β genes of the single HLA-DQ2.2:DQ2.2-glut-L1 tetramer binding CD4+ T cells isolated from six T-cell lines (TCLs) of four Celiac disease patients.

  Dataset EGAD00001005047

• RNA sequencing of tumor samples from patients with Waldenstrom macroglobulinemia

  RNA was extracted from flow-sorted CD19+. RNA-Seq was performed on 32 samples of 30 patients (2 replicates per samples). RNA-Seq libraries were subjected to non-stranded paired-end (2 x 75 bp) sequencing on HiSeq 2500 (Illumina). The files are in FASTQ format.

  Dataset EGAD00001005324

• Predictor_ChemoNEAR_TNBC (2019-08-14)

  In this study a collection of core biopsies from breast cancer patients receiving neoadjuvant chemotherapy as part of the ChemoNEAR trial will be investigated. The study is intended to detect early acquired resistance in women with diagnosed breast carcinoma. Samples will undergo whole genome sequencing and analysis, including use of HR Predict. . This dataset contains all the data available for this study on 2019-08-14.

  Dataset EGAD00001005255

• Natural Killer Cell Plasticity During IL-15-driven Homeostatic Proliferation

  Here we performed single-cell RNA sequencing to address repertoire stability and subset plasticity during IL-15 driven homeostatic proliferation. Sorted NK cell subsets representing discrete stages of NK cell differentiation are compared with the corresponding subsets after proliferation and further sorted into two subsets depending on the rate of proliferation.

  Dataset EGAD00001005420

• LBC1936 VCF

  LBC1921 and LBC1936 GVCFs called with GATK's HaplotypeCaller were combined and subject to variant quality score recalibration. This VCF contains the subset of samples (n = 1068) from the LBC1936 cohort.

  Dataset EGAD00001005478

• Validation data for the SV analysis package: GRIDSS, PURPLE, LINX

  Validation data containing sequencing data of 13 samples. An hybrid capture approach was used to validate findings of both Manta and GRIDSS for the samples in the validation set. The dataset also contains the reference sequences used.

  Dataset EGAD00001005525

• DESIGN II HNSCC RNA-Seq

  RNA-Seq data of 28 HPV-negative HNSCC specimens from patients treated at the Netherlands Cancer Institute (Amsterdam), VU Medical Centre (Amsterdam) or MAASTRO Clinic (Maastricht) in The Netherlands. HNSCC biopsy samples were obtained prior to treatment (chemo-radiotherapy) for the prospective study within the DESIGN project and used for polyA mRNA sequencing.

  Dataset EGAD00001005722

• Long read sequencing of 5 Intellectual Disability (ID) trios with PacBio Sequel. Dataset of samples: T2P, T2F and T2M

  5 trios were whole genome sequenced with PacBio Sequel to a depth of 15X (Trios 1-4) or 40X (Trio 5). For each trio the child was affected with severe ID, and the parents were unaffected. Dataset consists of Trio 2 samples: T2P, T2F and T2M

  Dataset EGAD00001006050

• Collection of Genotypic and Ethnographic Information from Individuals of South African Ethnic Groups

  Whole genome sequencing data of 84 Nama individuals with KhoeSan ancestry from southern Africa in phased VCF format. Variants were called/phased as part of the African Genome Resource. The data has been aligned to GRCh37.

  Dataset EGAD00001006198